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Last updated: August 24, 2009


DOCSS

 

DOCSS

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  The Database of Chemical Stability Space (DOCSS) a database of biochemical reaction networks that exhibit bistability. The database is curated using the results of the publication "N. Ramakrishnan and U.S. Bhalla, Memory Switches in Chemical Reaction Space", PLoS Computational Biology, Vol. 4, No. 7, July 2008.

 

Model hierarchy

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     Class     
       
  ↓
       
     Configuration     
       
  ↓
       
     Model     
       
       
     
  Solution       eigens  
     



 Class
 The model class is specified by the name: mXn where
  -m stands for number of molecule,
  -n stands for number of reaction.

 Configuration
  The M specifies the configure number of a model, a unique id within each class.

 Model
  For a given configuration there may be many models.

 Solution
  Here we list the concentrations of the molecules at the solved steady-state.

 eigens
  This lists the eigenvalues.
  Depending on the eigens value the solution are classfied as  stable, saddle, unstable, line or  doublet.

Presearch Result

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These are list of presearch result of bistable models.
Click mXn.bistable set from the List of bistable models for presearch result, where m is molecule and n are reaction.


Search Types

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  • Banyan Tree  

    • Each node in banyan tree diagram represents bistable model and node color represents bistability propensity.

      Click on these nodes to get the details of bistable model.



  • Basic Search 

      The query searches only bistable model.

    • For minimum search
      - Number of molecules,
      - Number of reactions and
      - Propensity range is required.

    • Query terms can be qualified using Search Fields.



  • AdvanceSearch 

      The query searches all the models in the database.

    • For minimum search
      - Number of molecules,
      - Number of reactions and
      - Propensity range is reqiured.

    • In addtion to minimum search requirement, query can be qualified using additional Search Fields.



  • Search Tags 

      Query terms on DOCSS can be qualified using case insensitive search tags for different Search Fields

      Search Field Qualifiers:

    • Molecule Used, to search model on molecule bases.

    • Reaction Used, to search model on reaction bases.

    • Propensity a range from 0 to 1 must be provided for searching.

    • Solution Used, to search number of solution for a given model.

    • Stable Used, to specify number of bistable for a given model.

    • Signature Used, to search string for a given model.


      Match Field Qualifiers

    • Equal Used, to search query term for equal to.

    • Great Used, to search query term for great value.

    • Any Used, to search for the query term found anywhere within the string.

    • Exact Used, to run a search for the exact word.


 

SearchBar

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  The Search bar on DOCSS page provides access to additional search options. Use of the relevant options allows to limit your retrieval to a specific subset of data within DOCSS.

Search Field

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  • Molecule  
    From the drop down menu of the search field "Number of Molecules" select the "#" and press the Entry key or click Submit. Depending on the # of Molecules the result will display models from class.
    To get all the models from the data set select "Any" from the "Number of Molecules"
    Default value is 2 (two).


  • Reaction 
    From the drop down menu of the search field "Number of Reaction" select the "#" and press the Entry key or click Submit. Depending on the # of Reaction the result will display models from class.
    To get all the models from the data set select "Any" from the "Number of Reaction"
    Default value is 1 (one).


  • Propensity 

      Propensity value ranges from 0 to 1 and for searching both Upper and lower bound should be provided. Default value for lower bound is 0 (Zero) and upper bound is 1 (one).

    Propensity =
    Number of bistable for a given model for a given class

    Total number of models for a given class


  • Solution  

    Enter a numeric value for searching number of solution for a given model.


  • Stable  

    Enter a numeric value for searching number of bistable models.


  • Signature  

  • The search string should start and end with delimiter vertical bars '|', the first letter of the signature specifies the reaction from the signature list below, and the following lower case letters identify the molecules. X indicates that the reaction only involves two molecules so there is no third entry.
    The signature list AabX, BabX, CabX, DabX, Eabc, Fabc, Gabc, Habc, Iabc, Jabc, Kabc, Labc

  • One can add multipy such signature by vertical bar '|' as delimiter. E.g |Fabc|CabX|.



 

Match Field

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  • Equal  
    For # molecule, # reaction,# solution #stable state DOCSS selects data whose Search Field values are exactly the same as the search string.

    • Default value of molecule is 2 and for reaction 1.

    • For # Solution, # stable state user defined value are taken.Selects documents whose document field values are greater than the search string you specify

  • Great  
    For # molecule, # reaction,# solution #stable state DOCSS selects data whose Search Field values are greater than the search string.

    • Default value of molecule is 2 and for reaction 1.

    • For # Solution, # stable state user defined value are taken.

  • Any  

      Default DOCSS search looks for the query term anywhere in the string. When the Any is selected from the radio button menu or when default searches are run, DOCSS is queried for any form of occurrence of the query term. E.g. When DOCSS is searched for CabX the actual search is done for wild card CabX wild card and this will yield |AabX|CabX|, CabX and |CabX|Dbca|EbcX| in the search results.

  • Exact  

      When the Match field parameter Exact is selected from the radio button menu and the searches are run, DOCSS is queried for the occurrence of the exact query term. E.g. When an Exact search is executed for CabX, the actual search is done exactly for CabX and this will yield only |CabX| in the search results and not |AcaX|CabX| or |CabX|Labc|.




DOCSS Team